Analysis of comprehensive genomic profiling of solid tumors with a novel assay for broad analysis in clinical diagnostics
Somatic multigene analysis by next‐generation sequencing (NGS) is routinely integrated in medical oncology for clinical decision‐making. However, with the fast‐growing number of recommended and required genes as well as pan‐cancer biomarkers, small panels have become vastly insufficient. Comprehensi...
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| Main Authors: | , , , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Wiley
2025-06-01
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| Series: | Molecular Oncology |
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| Online Access: | https://doi.org/10.1002/1878-0261.13812 |
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| author | Guy Froyen Pieter‐Jan Volders Ellen Geerdens Severine Berden Joni Van der Meulen Aaron De Cock Stefanie Vermeire Jacques Van Huysse Marie deBarsy Gabriela Beniuga Wendy W. J. deLeng Anne M. L. Jansen Imke Demers Zeliha Ozgur Hendrikus Jan Dubbink Ernst‐Jan M. Speel Wilfred F. J. vanIJcken Brigitte Maes |
| author_facet | Guy Froyen Pieter‐Jan Volders Ellen Geerdens Severine Berden Joni Van der Meulen Aaron De Cock Stefanie Vermeire Jacques Van Huysse Marie deBarsy Gabriela Beniuga Wendy W. J. deLeng Anne M. L. Jansen Imke Demers Zeliha Ozgur Hendrikus Jan Dubbink Ernst‐Jan M. Speel Wilfred F. J. vanIJcken Brigitte Maes |
| author_sort | Guy Froyen |
| collection | DOAJ |
| description | Somatic multigene analysis by next‐generation sequencing (NGS) is routinely integrated in medical oncology for clinical decision‐making. However, with the fast‐growing number of recommended and required genes as well as pan‐cancer biomarkers, small panels have become vastly insufficient. Comprehensive genomic profiling (CGP) is, thus, required to screen for clinically relevant markers. In this multicentric study, we report on an extensive analysis across seven centers comparing the results of the novel OncoDEEP CGP assay with the diagnostically validated TruSight Oncology 500 (TSO500) kit on 250 samples. Overall concordance was 90% for clinically relevant gene variants and >96% for more complex biomarkers. Agreement for fusion detection was 94% for the 11 overlapping clinically actionable driver genes. The higher coverage uniformity of OncoDEEP compared to TSO500 allows users to pool more samples per sequencing run. Tertiary data analysis, including reporting, is integrated in the OncoDEEP solution, whereas this is an add‐on for TSO500. Finally, we showed that, analytically, the OncoDEEP panel performs well, thereby advocating its use for CGP of solid tumors in diagnostic laboratories, providing an all‐in‐one solution for optimal patient management. |
| format | Article |
| id | doaj-art-568ae17c42ee4fdf91b9ab88fc830551 |
| institution | Kabale University |
| issn | 1574-7891 1878-0261 |
| language | English |
| publishDate | 2025-06-01 |
| publisher | Wiley |
| record_format | Article |
| series | Molecular Oncology |
| spelling | doaj-art-568ae17c42ee4fdf91b9ab88fc8305512025-08-20T03:44:52ZengWileyMolecular Oncology1574-78911878-02612025-06-011961797181010.1002/1878-0261.13812Analysis of comprehensive genomic profiling of solid tumors with a novel assay for broad analysis in clinical diagnosticsGuy Froyen0Pieter‐Jan Volders1Ellen Geerdens2Severine Berden3Joni Van der Meulen4Aaron De Cock5Stefanie Vermeire6Jacques Van Huysse7Marie deBarsy8Gabriela Beniuga9Wendy W. J. deLeng10Anne M. L. Jansen11Imke Demers12Zeliha Ozgur13Hendrikus Jan Dubbink14Ernst‐Jan M. Speel15Wilfred F. J. vanIJcken16Brigitte Maes17Laboratory for Molecular Diagnostics, Department of Clinical Biology Jessa Hospital Hasselt BelgiumLaboratory for Molecular Diagnostics, Department of Clinical Biology Jessa Hospital Hasselt BelgiumLaboratory for Molecular Diagnostics, Department of Clinical Biology Jessa Hospital Hasselt BelgiumLaboratory for Molecular Diagnostics, Department of Clinical Biology Jessa Hospital Hasselt BelgiumDepartment of Biomolecular Medicine Ghent University Ghent BelgiumMolecular Diagnostics Ghent University Hospital (MDG) Ghent University Hospital Ghent BelgiumDepartment of Pathology AZ Sint‐Jan Brugge AV Bruges BelgiumDepartment of Pathology AZ Sint‐Jan Brugge AV Bruges BelgiumInstitute of Pathology and Genetics (IPG) Gosselies BelgiumInstitute of Pathology and Genetics (IPG) Gosselies BelgiumDepartment of Pathology University Medical Centre Utrecht The NetherlandsDepartment of Pathology University Medical Centre Utrecht The NetherlandsDepartment of Pathology Maastricht University Medical Center Maastricht The NetherlandsGenomics Core Facility Erasmus University Medical Center Rotterdam The NetherlandsDepartment of Pathology Erasmus MC Cancer Institute Rotterdam The NetherlandsDepartment of Pathology Maastricht University Medical Center Maastricht The NetherlandsGenomics Core Facility Erasmus University Medical Center Rotterdam The NetherlandsLaboratory for Molecular Diagnostics, Department of Clinical Biology Jessa Hospital Hasselt BelgiumSomatic multigene analysis by next‐generation sequencing (NGS) is routinely integrated in medical oncology for clinical decision‐making. However, with the fast‐growing number of recommended and required genes as well as pan‐cancer biomarkers, small panels have become vastly insufficient. Comprehensive genomic profiling (CGP) is, thus, required to screen for clinically relevant markers. In this multicentric study, we report on an extensive analysis across seven centers comparing the results of the novel OncoDEEP CGP assay with the diagnostically validated TruSight Oncology 500 (TSO500) kit on 250 samples. Overall concordance was 90% for clinically relevant gene variants and >96% for more complex biomarkers. Agreement for fusion detection was 94% for the 11 overlapping clinically actionable driver genes. The higher coverage uniformity of OncoDEEP compared to TSO500 allows users to pool more samples per sequencing run. Tertiary data analysis, including reporting, is integrated in the OncoDEEP solution, whereas this is an add‐on for TSO500. Finally, we showed that, analytically, the OncoDEEP panel performs well, thereby advocating its use for CGP of solid tumors in diagnostic laboratories, providing an all‐in‐one solution for optimal patient management.https://doi.org/10.1002/1878-0261.13812comprehensive genomic profiling (CGP)diagnostic assay validationnext‐generation sequencing (NGS)solid tumors |
| spellingShingle | Guy Froyen Pieter‐Jan Volders Ellen Geerdens Severine Berden Joni Van der Meulen Aaron De Cock Stefanie Vermeire Jacques Van Huysse Marie deBarsy Gabriela Beniuga Wendy W. J. deLeng Anne M. L. Jansen Imke Demers Zeliha Ozgur Hendrikus Jan Dubbink Ernst‐Jan M. Speel Wilfred F. J. vanIJcken Brigitte Maes Analysis of comprehensive genomic profiling of solid tumors with a novel assay for broad analysis in clinical diagnostics Molecular Oncology comprehensive genomic profiling (CGP) diagnostic assay validation next‐generation sequencing (NGS) solid tumors |
| title | Analysis of comprehensive genomic profiling of solid tumors with a novel assay for broad analysis in clinical diagnostics |
| title_full | Analysis of comprehensive genomic profiling of solid tumors with a novel assay for broad analysis in clinical diagnostics |
| title_fullStr | Analysis of comprehensive genomic profiling of solid tumors with a novel assay for broad analysis in clinical diagnostics |
| title_full_unstemmed | Analysis of comprehensive genomic profiling of solid tumors with a novel assay for broad analysis in clinical diagnostics |
| title_short | Analysis of comprehensive genomic profiling of solid tumors with a novel assay for broad analysis in clinical diagnostics |
| title_sort | analysis of comprehensive genomic profiling of solid tumors with a novel assay for broad analysis in clinical diagnostics |
| topic | comprehensive genomic profiling (CGP) diagnostic assay validation next‐generation sequencing (NGS) solid tumors |
| url | https://doi.org/10.1002/1878-0261.13812 |
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